Correct, I don't currently do anything to either support the DEC mod or even support or tested with generally deleting chunks, but how you described it is how I'd expect it to behave.
@PiggyWisky: I wouldn't be surprised if you're close right in terms of runtime CPU (at least for biter free worlds), but I think DEC still has significant impact on save file size, which I think empty chunks can still play a big role in. And having played games where saving takes 30+ seconds, it can be a big thing.
I think I can do some saving of positions and then everytime a new chunk checks I'd check it against a list of archived buildings when new chunks are spawned to see if there are buildings I need to respawn. I can probably ignore respawning recipe or rotation information, but it'll still take a bit of work and I need to put it lower on my priority list as I have a few other features that people keep bugging me for that I haven't gotten around to implementing.